Research workbench
Structure of the extracellular domain of human csf-1 receptor in complex with the Fab fragment of RG7155
Analyse Structure of the extracellular domain of human csf-1 receptor in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LIQ
- Type
- protein
- Length
- 894 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrophage colony-stimulating factor 1 receptor; Fab fragment RG7155 heavy chain; Fab…
- EC
- 2.7.10.1
- UniProt
- P07333
- Ligands
- NAG, FUC, BMA, SO4
- Pockets
- 7 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Macrophage colony-stimulating factor 1 receptor (EC 2.7.10.1) | protein | 469 | 3% helix, 57% strand | P07333 |
| H | Fab fragment RG7155 heavy chain | protein | 212 | 9% helix, 52% strand | — |
| L | Fab fragment RG7155 light chain | protein | 213 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains E
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains E
- BMA · beta-D-mannopyranose · sugar
- SO4 · Sulfate ion · ion · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.54 | 0.78 | 38 | empty |
| 2 | 334 | 0.53 | 0.74 | 48 | empty |
| 3 | 176 | 0.49 | 0.77 | 31 | empty |
| 4 | 166 | 0.44 | 0.75 | 25 | empty |
| 5 | 104 | 0.37 | 0.74 | 22 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1665 Ų buried · 13 hydrogen bonds · protein-protein
- E–H · 675 Ų buried · 12 hydrogen bonds · protein-protein
- E–L · 382 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4LIQ · Structure of the extracellular domain of human CSF-1 receptor in complex with the Fab… · the same entry in another collection · chain E against E, TM-score 1.00
- P07333 · AlphaFold monomer V2.0 prediction for macrophage colony-stimulating factor 1 receptor… · a predicted model of the same protein · chain E against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P07333
- Elsewhere: RCSB PDB 4LIQ · PDBe 4LIQ · UniProt P07333
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